database_selection_guide.md

Database Selection Guide

Which database answers which question, grouped by domain: physics and astronomy, earth and environmental sciences, chemistry and drugs, materials science and crystallography, biology and genomics, disease and clinical, patents and regulatory, economics and finance, social sciences and demographics, and cross-domain queries.

Database Selection Guide

Match the user's intent to the right database(s). Many queries benefit from hitting multiple databases.

Physics & Astronomy

User is asking about...	Primary database(s)	Also consider
Near-Earth objects, asteroids	NASA (NeoWs)	—
Mars rover images	NASA (Mars Rover Photos)	—
Exoplanets, orbital parameters	NASA Exoplanet Archive	—
Astronomical objects by name/coordinates	SIMBAD	SDSS
Galaxy/star spectra, photometry	SDSS	SIMBAD
Physical constants	NIST	—
Atomic spectra, spectral lines	NIST (ASD)	—

Earth & Environmental Sciences

User is asking about...	Primary database(s)	Also consider
Earthquakes, seismic events	USGS Earthquakes	—
Water data, streamflow, groundwater	USGS Water Services	—
Weather (current, forecast, historical)	OpenWeatherMap	NOAA
Climate data, historical weather stations	NOAA (CDO)	—
Air quality, toxic releases	EPA (Envirofacts)	—

Chemistry & Drugs

User is asking about...	Primary database(s)	Also consider
Chemical compounds, molecules	PubChem	ChEMBL
Molecular properties (weight, formula, SMILES)	PubChem	—
Drug synonyms, CAS numbers	PubChem (synonyms)	DrugBank
Bioactivity data, IC50, binding assays	ChEMBL	BindingDB, PubChem
Drug binding affinities (Ki, IC50, Kd)	ChEMBL, BindingDB	PubChem
Drug-target interactions	ChEMBL, DrugBank	BindingDB, Open Targets
Ligands for a protein target (by UniProt)	BindingDB	ChEMBL
Target identification from compound structure	BindingDB (SMILES similarity)	ChEMBL
Drug labels, adverse events, recalls	FDA (OpenFDA)	DailyMed
Drug labels (structured product labels)	DailyMed	FDA (OpenFDA)
Drug pharmacology, indications	DrugBank	FDA
Chemical cross-referencing	PubChem (xrefs)	ChEMBL
Commercially available compounds for screening	ZINC	PubChem
Similarity/substructure search (purchasable)	ZINC	PubChem, ChEMBL
Drug-like compound libraries, building blocks	ZINC	—
FDA-approved drug structures	ZINC (fda subset)	PubChem, FDA
Compound purchasability, vendor catalogs	ZINC	—

Materials Science & Crystallography

User is asking about...	Primary database(s)	Also consider
Materials by formula or elements	Materials Project	COD
Band gap, electronic structure	Materials Project	—
Crystal structures, CIF files	COD	Materials Project
Elastic/mechanical properties	Materials Project	—
Formation energy, thermodynamics	Materials Project	—
Cell parameters, space groups	COD	Materials Project

Biology & Genomics

User is asking about...	Primary database(s)	Also consider
Biological pathways	Reactome, KEGG	—
What pathways a gene/protein is in	Reactome (mapping), KEGG	—
Enzyme kinetics, catalytic activity	BRENDA	KEGG
Metabolomics studies, metabolite profiles	Metabolomics Workbench	PubChem
m/z or exact mass lookup	Metabolomics Workbench (moverz/exactmass)	PubChem
Protein sequence, function, annotation	UniProt	Ensembl
Protein-protein interactions	STRING	BioGRID
Gene information, genomic location	NCBI Gene	Ensembl
Genome sequences, variants, transcripts	Ensembl	NCBI Gene
Gene expression datasets	GEO (NCBI E-utilities)	—
Gene expression across tissues	GTEx	Human Protein Atlas
Gene expression signatures (CMap/L1000)	LINCS L1000	GEO
Gene set enrichment vs GEO	RummaGEO	GEO
Protein sequences (NCBI)	NCBI Protein	UniProt
Taxonomic classification	NCBI Taxonomy	—
SNP/variant data (dbSNP)	dbSNP	ClinVar, gnomAD
Population variant frequencies	gnomAD	dbSNP
Sequencing run metadata	SRA	ENA, GEO
Nucleotide sequences (European archive)	ENA	SRA, NCBI Gene
Genome assemblies, raw reads (European)	ENA	SRA, Ensembl
Cross-references from sequence accessions	ENA (xref)	NCBI Gene, UniProt
Viral sequence datasets with NCBI Virus-style filters	gget virus deterministic layer	SRA, ENA, NCBI Protein
Genome annotations, tracks	UCSC Genome Browser	Ensembl
3D protein structures (experimental)	PDB (RCSB)	EMDB
3D protein structures (predicted)	AlphaFold DB	PDB
EM maps, cryo-EM structures	EMDB	PDB
Protein families, domains	InterPro	UniProt
Chemical entities (biological)	ChEBI	PubChem
Protein/genetic interactions	BioGRID	STRING
Gene function annotations (GO terms)	QuickGO	Gene Ontology
Regulatory elements, ChIP-seq, ATAC-seq	ENCODE	—
TF binding profiles/motifs	JASPAR	ENCODE
Protein expression across tissues	Human Protein Atlas	UniProt
Single-cell atlas projects	Human Cell Atlas	—
Proteomics datasets	PRIDE	—
Mouse gene data	MouseMine	NCBI Gene
Plasmid repository	Addgene	—

Organism/species matters. Most biology databases cover multiple organisms. If the user's query is about a specific organism, pass it explicitly — don't assume human. Common patterns: Ensembl uses {species} in the URL path (e.g. homo_sapiens), STRING/BioGRID/QuickGO use NCBI taxon IDs (species=9606 for human, 10090 for mouse), UniProt uses organism_id:9606 in search queries, KEGG uses organism codes (hsa, mmu). GTEx and Human Protein Atlas are human-only. Check the reference file for each database's specific parameter.

Viral sequence retrieval is high risk. For NCBI Virus-style requests with filters such as host, geography, collection dates, sequence length, completeness, ambiguous bases, segment, lab passage, source database, or protein annotation, prefer the gget skill's gget virus deterministic retrieval layer over hand-assembling browser or API workflows. If you must use SRA/ENA/NCBI APIs directly, document which filters were enforced server-side and which were validated locally, then reconcile final accession counts.

Disease & Clinical

User is asking about...	Primary database(s)	Also consider
Somatic mutations in cancer	COSMIC	Open Targets, cBioPortal
Cancer genomics (TCGA)	GDC (TCGA)	COSMIC, cBioPortal
Cancer study mutations, CNA, expression	cBioPortal	GDC (TCGA), COSMIC
Tumor clinical data (survival, staging)	cBioPortal	GDC (TCGA)
Drug-target-disease associations	Open Targets	ChEMBL
Gene-disease associations	DisGeNET	Open Targets, Monarch
Mendelian disease-gene relationships	OMIM	NCBI Gene
Variant clinical significance	ClinVar (NCBI)	OMIM
GWAS SNP-trait associations	GWAS Catalog	—
Disease-phenotype-gene links	Monarch Initiative	HPO
Phenotype ontology, HPO terms	HPO	Monarch
Pharmacogenomics, drug-gene interactions	ClinPGx (PharmGKB)	DrugBank
Clinical trials for a drug/disease	ClinicalTrials.gov	FDA
Disease-related expression data	GEO	Open Targets

Patents & Regulatory

User is asking about...	Primary database(s)	Also consider
Patents by keyword or technology	USPTO ODP PatentsView bulk (PatentSearch API paused)	—
Patents by inventor or assignee	USPTO ODP PatentsView bulk (PatentSearch API paused)	—
Patent prosecution status	USPTO (PEDS)	—
Trademark lookup	USPTO (TSDR)	—
SEC company filings, 10-K, 10-Q	SEC EDGAR	—

Economics & Finance

User is asking about...	Primary database(s)	Also consider
US economic time series (GDP, CPI, rates)	FRED	BEA
Employment, wages, labor statistics	BLS	FRED
GDP, national accounts	BEA	FRED, World Bank
International development indicators	World Bank	FRED
Interest rates, money supply	Federal Reserve	FRED
Euro exchange rates, ECB monetary stats	ECB	—
US debt, yield curves, fiscal data	US Treasury	FRED
Stock prices, forex, crypto	Alpha Vantage	—
Statistical data across many topics	Data Commons	—

Social Sciences & Demographics

User is asking about...	Primary database(s)	Also consider
US population, housing, income data	US Census	Data Commons
EU statistics (economy, trade, health)	Eurostat	World Bank
Global health indicators (mortality, disease)	WHO GHO	World Bank

Cross-domain queries

User is asking about...	Primary database(s)	Also consider
Everything about a compound	PubChem + ChEMBL + DrugBank	BindingDB, ZINC, Reactome, FDA
Everything about a gene	NCBI Gene + UniProt + Ensembl	Reactome, STRING, COSMIC, cBioPortal, ENA
Everything about a variant	dbSNP + ClinVar + gnomAD	GWAS Catalog, COSMIC, cBioPortal
Drug target pathways	ChEMBL + Reactome	Open Targets, GEO
Prior art for a chemical invention	USPTO + PubChem	ChEMBL
Everything about a material	Materials Project + COD	—
US economic overview	FRED + BLS + BEA	Federal Reserve

When the user's query spans multiple domains (e.g. "what do we know about aspirin" or "find everything about BRCA1"), rank sources by authority and start with the 2-3 databases most likely to answer the question. Add more databases only when the first pass leaves a specific gap. Keep at most 5 independent API requests in flight at once.